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Badly formatted epubs can cause the slowness and too many books on the device even with enough free ram as you said, it still takes time to index the books (when I hit around 1000 books on my 350, I noticed a considerable slowdown in everything, even turning pages within a book).
I'd suggest a factory reset first to clear out all the old files and notes from deleted books, and then load the books again and see if performance doesn't improve.
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